fix: Resolve MCP package shadowing issue and add package structure tests

🐛 Fixes:
- Fix mcp package shadowing by importing external MCP before sys.path modification
- Update mcp/server.py to avoid shadowing installed mcp package
- Update tests/test_mcp_server.py import order

✅ Tests Added:
- Add tests/test_package_structure.py with 23 comprehensive tests
- Test cli package structure and imports
- Test mcp package structure and imports
- Test backwards compatibility
- All package structure tests passing ✅

📊 Test Results:
- 205 tests passed ✅
- 67 tests skipped (PDF features, PyMuPDF not installed)
- 23 new package structure tests added
- Total: 272 tests (excluding test_mcp_server.py which needs more work)

⚠️ Known Issue:
- test_mcp_server.py still has import issues (67 tests)
- Will be fixed in next commit
- Main functionality tests all passing

Impact: Package structure working, 75% of tests passing

tests/test_mcp_server.py

@@ -14,10 +14,8 @@ import asyncio
 from pathlib import Path
 from unittest.mock import Mock, patch, AsyncMock, MagicMock
 
-# Add parent directory to path
-sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-
-# Import MCP package components (from installed package)
+# CRITICAL: Import MCP package BEFORE adding project to path
+# to avoid shadowing the installed mcp package with our local mcp/ directory
 try:
     from mcp.server import Server
     from mcp.types import Tool, TextContent
@@ -26,6 +24,9 @@ except ImportError:
     MCP_AVAILABLE = False
     print("Warning: MCP package not available, skipping MCP tests")
 
+# NOW add parent directory to path for importing our local modules
+sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+
 # Import our local MCP server module
 if MCP_AVAILABLE:
     # Add mcp directory to path to import our server module